Dataset Information

Catalog of genetic variants within mature microRNA seed regions in chicken.

ABSTRACT: MicroRNA (miRNA) is a class of noncoding RNA important in posttranscriptional regulation of target genes. The regulation mechanism requires complementarity between target mRNA and the miRNA region responsible for their recognition and binding, also called the seed region. It has been estimated that each miRNA targets approximately 200 genes and genetic variability of miRNA genes has been associated with phenotypic variation and disease susceptibility in humans, livestock species, and model organisms. Polymorphisms in miRNA genes especially within the seed region could therefore represent biomarkers for phenotypic traits important in livestock animals. Using the updated Version 5.0 of our previously developed bioinformatics tool miRNA SNiPer we assembled polymorphic miRNA genes in chicken. Out of 740 miRNA genes 263 were polymorphic, among them 77 had SNPs located within the mature region, and 29 of them within the miRNA seed region. Because several polymorphisms in databases result from sequencing errors, we performed experimental validation of polymorphisms located within 4 selected miRNA genes in chicken (gga-mir-1614, -1644, -1648, and -1657). We confirmed the presence of nine polymorphisms and identified 3 additional novel polymorphisms within primary miRNA regions in chicken representing 3 layer-type breeds, one layer-type hybrid, and one meat-type intercrossed population. The developed catalog of mir-SNPs in chicken can serve researchers as a starting point for association studies dealing with poultry production traits and designing functional experiments.

SUBMITTER: Zorc M

PROVIDER: S-EPMC4988550 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

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Catalog of genetic variants within mature microRNA seed regions in chicken.

Zorc Minja M Omejec Sandra S Tercic Dusan D Holcman Antonija A Dovc Peter P Kunej Tanja T

Poultry science 20150713 9

MicroRNA (miRNA) is a class of noncoding RNA important in posttranscriptional regulation of target genes. The regulation mechanism requires complementarity between target mRNA and the miRNA region responsible for their recognition and binding, also called the seed region. It has been estimated that each miRNA targets approximately 200 genes and genetic variability of miRNA genes has been associated with phenotypic variation and disease susceptibility in humans, livestock species, and model organ ...[more]

PMID: 26175051

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Project description:Meat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particular genomic footprints throghtout the genome. Thus, the aims of this study were to sequence 28 chickens from two Brazilian lines (meat and white egg-type) and use this information to characterize genome-wide genetic variations, identify putative regions under selection using Fst method, and find putative pathways under selection.A total of 13.93 million SNPs and 1.36 million INDELs were identified, with more variants detected from the broiler (meat-type) line. Although most were located in non-coding regions, we identified 7255 intolerant non-synonymous SNPs, 512 stopgain/loss SNPs, 1381 frameshift and 1094 non-frameshift INDELs that may alter protein functions. Genes harboring intolerant non-synonymous SNPs affected metabolic pathways related mainly to reproduction and endocrine systems in the white-egg layer line, and lipid metabolism and metabolic diseases in the broiler line. Fst analysis in sliding windows, using SNPs and INDELs separately, identified over 300 putative regions of selection overlapping with more than 250 genes. For the first time in chicken, INDEL variants were considered for selection signature analysis, showing high level of correlation in results between SNP and INDEL data. The putative regions of selection signatures revealed interesting candidate genes and pathways related to important phenotypic traits in chicken, such as lipid metabolism, growth, reproduction, and cardiac development.In this study, Fst method was applied to identify high confidence putative regions under selection, providing novel insights into selection footprints that can help elucidate the functional mechanisms underlying different phenotypic traits relevant to meat and egg-type chicken lines. In addition, we generated a large catalog of line-specific and common genetic variants from a Brazilian broiler and a white egg layer line that can be used for genomic studies involving association analysis with phenotypes of economic interest to the poultry industry.

Dataset Information

Catalog of genetic variants within mature microRNA seed regions in chicken.

Publications

Catalog of genetic variants within mature microRNA seed regions in chicken.

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